Methods and devices are provided for pretreatment of a sample containing microbial cells. In some embodiments, the pretreatment of the sample is performed via the initial selective lysis, within a sample pretreatment vessel, of non-microbial cells (such as blood cells) and the subsequent centrifugal separation of the sample to remove the resulting debris and concentrate the microbial cells. An immiscible and dense cushioning liquid may be included for collecting the microbial cells adjacent to the liquid interface formed by the cushioning liquid upon centrifugation of the pretreatment vessel. After removal of a substantial quantity of the supernatant, resuspension of the collected microbial cells, and re-establishment of the cushioning liquid interface, at least a portion of the remaining suspension may be removed without substantially removing the cushioning liquid. One or more intermediate wash cycles may be performed prior to extraction of the remaining suspension, which provides a “pretreated” sample.

Disclosed are systems and methods for detecting genetic alterations comprising androgen receptor gene splice variants (AR-Vs), mutations, indel, copy number changes, fusion and combination thereof, in a biofluid sample from the patient. The systems and methods are similarly applicable to the detection of gene alterations comprising gene splicing variants, mutations, indel, copy number changes, fusion and combination thereof of other genes of interest. The streamlined methods improve the consistency and simplicity of non-invasive detections of biomarkers.

The present application relates to a nucleic acid purification method, specifically to a nucleic acid purification method which includes a first step of crystallizing the nucleic acid using a solution containing a hydrophilic organic solvent; and a second step of drying the crystallized nucleic acid with high-humidity hot air.

Methods are disclosed for treating a subject with a tumor. These methods include administering to the subject a therapeutically effective amount of CD8.sup.+CD39.sup.+CD103.sup.+ T cells. Methods also are disclosed for isolating a nucleic acid encoding a T cell receptor (TCR) that specifically binds a tumor cell antigen. These methods include isolating CD8.sup.+CD39.sup.+CD103.sup.+ T cells from a sample from a subject with a tumor expressing the tumor cell antigen, and cloning a nucleic acid molecule encoding a TCR from the CD8.sup.+CD39.sup.+CD103.sup.+ T cells. In addition, methods are disclosed for expanding CD8.sup.+CD39.sup.+CD103.sup.+ T cells. In additional embodiments, methods are disclosed for determining if a subject with a tumor will respond to a checkpoint inhibitor. The methods include detecting the presence of CD8.sup.+CD39.sup.+CD103.sup.+ T cells in a biological sample from a subject.

Systems, methods, and apparatuses for generating and using machine learning models using genetic data. A set of input features for training the machine learning model can be identified and used to train the model based on training samples, e.g., for which one or more labels are known. As examples, the input features can include aligned variables (e.g., derived from sequences aligned to a population level or individual references) and/or non-aligned variables (e.g., sequence content). The features can be classified into different groups based on the underlying genetic data or intermediate values resulting from a processing of the underlying genetic data. Features can be selected from a feature space for creating a feature vector for training a model. The selection and creation of feature vectors can be performed iteratively to train many models as part of a search for optimal features and an optimal model.

DNA is sequenced by: (a) combining dsDNA fragments with Y-adapters and hairpin adapters comprising an affinity-label under conditions wherein the adapters ligate to fragments forming a mixture of fragment inserts flanked by two Y-adapters, a Y-adapter and a hairpin adapter, and two hairpin adapters; and (b) sequencing the selected fragment inserts with sequencing primers selecting for the Y-adapters.

Methods, systems, and devices for sampling/isolating material from cells. An exemplary system may comprise a chip including an electrode array of sampling electrodes arranged along a surface of the chip. A cell-receiving area may be located adjacent the surface of the chip. The system also may comprise a tag array of tags supported by the chip and aligned with the electrode array. Each tag of the tag array may include an identifier that is unique to the tag within the tag array. Each tag may be configured to bind nucleic acids, or a capturing agent distinct from the tag may be aligned with each sampling electrode of the electrode array to capture a protein or other analyte of interest. The system further may comprise a control circuit configured to apply an individually controllable voltage to each sampling electrode of the electrode array and measure an electrical property of the sampling electrode.

Provided herein are methods and systems for identifying chromosomal structural variants in a preserved sample obtained from a subject using focused acoustic energy and chromosomal conformational capture. Also provided herein are methods and systems for relating the chromosomal structural variants identified from the preserved tissue sample to diseases or disorders, and methods of treating same.

Provided herein are methods and systems for identifying chromosomal structural variants in a preserved sample obtained from a subject using focused acoustic energy and chromosomal conformational capture. Also provided herein are methods and systems for relating the chromosomal structural variants identified from the preserved tissue sample to diseases or disorders, and methods of treating same.

The present disclosure relates to methods of analyzing and authenticating a sample from a subject. Benefits of the methods disclosed herein can include the detection of multiple analytes in a whole blood sample, and the quantitative measurement of amounts of multiple drugs, or their metabolites, present in a single low volume whole blood sample. A benefit of the methods disclosed herein can include a combination of analyzing drugs or metabolites in a blood sample, and authenticating the blood sample, or a body sample, as being taken from the subject. Additional benefits of the methods herein can be safe, secure, accurate, and reliable authentication of blood samples and other body samples from a subject.